the commander's heart
by fashiongirl97
Summary: Jenny Sheppard hasn't only been a federal agent, but a high ranking naval officer. When a case throws her and team Gibbs back onto that ship the secret begins to be revealed. Maybe it's time to face the fact her heart isn't in the job any more- jibbs r&r? #1 in the hearts trilogy
1. the secret begins to unravel

_**Disclaimer – I don't own NCIS **_

_**Authors Note – WOW! Another story from yours truly. I remember talking to Left my heart in paris about this months ago yet I'm only now finally writing it! I hope this is okay and that you enjoy!**_

_**So here it is!**_

It's strange really, you can know someone for years, and even decades yet never know even the smallest things. They'd known each other for years yet she didn't know if he had brothers, his mother's name. For him though, there was something slightly bigger that he didn't know. But why? Because we didn't ask, we don't wonder about the little things until it is too late.

_**-the captains heart-**_

Director Jenny Sheppard, a title she treasured yet one which had never truly been her dream. Being an agent, and investigator, sure it had been fun but she'd only done it, got there to avenge her father's death. She'd been in her late 20's when she had joined Jethro and his team. Falling for him had never been part of the plan; joining NCIS had never been pat of the plan. But even a decade later there is a massive part of her life he doesn't know about, a part she has removed from the files. It isn't bad, just something she didn't want broadcasting.

From an early age Jenny had been thrown into the world of the Navy. After her mother's death the summers were spend on Navy bases. But Jenny had soon gotten bored of playing with the navy brats and soon gotten her father to pull some strings. At the age of 14 she'd got herself into a Navy collide and in the summer trained with the seaman recruits. She got dirty looks but passed way above them. She had loved it – strangely enough. After finishing school she had already managed to reach the rank of a Petty Officer 3rd class which usually took years. Her father and she had known then that was what she wanted to do. Her smiled when she wore her full dress was as bright as day, when she saluted her eyes glistened. She always would remember the day that the Navy came to her school to talk to them all and she was stood there in her Seaman's uniform. Everyone had been shocked. She supposed it was a t an early age she had gotten ambition. She'd joined the navy full time after that and had somehow persuaded them to send her to college in between her tours of duty.

She remembered when she had climbed the ranks to a Lieutenant; the navy had been short on recruits that high up. Her and Captain Wayne Hoffman had been put in charge of a ship named: Destinies Peak. It had been the worst in the Navy, and where all those who were failing but had friends in high places were sent. Jenny and Wayne, over the course of 3 years turned it in to the best ship the US Navy had without firing any one. They had gotten respect, taught them rules and every one had been proud. Jenny had been congratulated by being given the rank of Commander; she had been the happiest ever. At the time she was the only female Commander in the US Navy and the youngest in history. She was proud, and Hoffman was of her. She stayed on for another year after that. Then she left for NCIS, dropping down the bottom of the food chain again without even a second thought. Her father's murder was on the books and she wanted revenge.

Yet now it was over a decade since she'd been Commander Jennifer Sheppard, and she missed hearing it. The reason she hated been called ma'am as a probie, was because it reminded her of what she had been. Other than Marrow and SecNav no one had known. Yet still in every meeting they begged her to return. 'Destinies Peak' was still the most awarded and best ship in the Navy. Every time they asked her to return her heart was screaming yes. The truth be known she had never been as happy as an agent as she was on that ship. She missed being part of a unit, the feeling that she really was serving her country not just signing paper work. Yet her head told her no.

This week though, it had been hard. The case Jethro's team had been about a Petty officer who had served on the ship was fond murdered in DC. Jenny had been shocked when Jethro had told her the name of the ship, but then she had talked with Hoffman, and they had agreed they would deal with it. Now she was stood in MTAC with him on the screen.

"Wayne, how are you?" she said with a genuine smile.

"Not bad commander." He said sarcastically.

"Director now and you know that."

"Sure I can't convince you to change that back."

"No. Now, my MCRT want access on your ship to interrogate, they aren't pleased. Neither am i."

"That there was a murder or that the ship we built is now under investigation."

"Both, what the hell happened Wayne?"

"I dunno Jen. I honestly don't. I swear though things are going back to how they were."

"I'm glad to hear it. Now the access?" she asked knowing there would be a deal. There always was, it was why they got on so well. Back in the days when they were building the ships reputation up again they had had to have a laugh otherwise they would have died from boredom. Even after Jenny left they'd kept in touch. They had become friends as well as colleagues. Since she'd gone he had stayed the same rank, not from a lack of promotion options.

"Jenny, I have one condition."

"And here I was thinking it would be straight forward…" she said in a joking tone.

"I've missed you Jenny! I want you to come with them, there is an award ceremony in 5 days, we're being awarded another award, the SecNav will be here. I want you to come, full uniform dress."

"You do realise that will give me away."

"Jenny, you built this ship up to what it is, you deserve to be here. So do that and your agents can come. Any of them from the service?"

"One, a marine."

"Tell him to bring his dress."

"You're on, but you owe me one Wayne."

"Think that's the opposite way around Jen."

"Yeah right. See you tonight."

"See ya Jen."

The screen went black and Jenny sighed, she guessed her secret was not going to be a secret much longer. A smile played on her lips; she was off back on her ship. That thought alone made her smile.

_**-the commanders heart-**_

Jenny Sheppard walked down the stairs to the bull pen, bag in hand. They all looked at her, waiting for the all clear to go on the ship. "You have permission from Captain Hoffman; you'll be there for 5/6 days flying out tonight, but on two conditions. Firstly I have to come with you, none of you question that."

"Secondly Jen?" asked Gibbs frustrated.

"Day 5, Ziva, Tony and McGee you will have to remain in your dorm room as there is a ceremony on, military personnel only. Jethro do you still have your uniform dressage?"

"Yeah."

"Right, you need to take it with you. We fly out in three hours; I want you all to meet me at the military airport, no luxury today."

With that she left. Jethro saw a hint of nerves in her eyes, he knew something was going on but didn't know whether to pry. They weren't much anymore, Jenny and Gibbs, he wasn't even sure if he could class her as a friend. She once had meant the world to him, but the job had gotten in the way, too many rubber chicken dinners had been put in front of her. She was still the same person, but he couldn't see her any more.

_**-the commanders heart-**_

Two and a half hours later Jenny was waiting for the agents. She had her duffle bag, which was near identical to Gibbs' as they'd bought them under cover years ago. She also had her unifuprm in its bag. She just hoped none of them saw it too soon. Jethro arrived, his duffle bag over his shoulder and uniform in hand. He looked at the black back she had with hers in confusion. "Later Jethro." She said, not feeling like explain that part of her life there and then. Within fifteen minutes the team was assembled and ready to go. Gibbs was surprised to see Jenny no in casual, yet kept quiet. She had changed into a pencil skirt that was knee length in a deep blue with matching blazer and a white shirt. She had her usual heals on yet the look was different, he just couldn't figure out how.

They boarded the plane, their bags put in holding before sitting down. Jenny and Gibbs ended up sitting next to each other. She glared at him not to mention anything embarrassing or else he would not survive the flight.

One and a half hours later they arrived at the boat. Jenny grabbed her stuff and led the way. They were all surprised that she knew her way as it had a different lay out to all the other ships. They entered and an older looking Chief Warrant Officer 5 looked at her in shock before whispering to his colleagues who she was. Soon they were all stood to attention. Jenny sighed; she had hoped no one would remember her. Wherever they walked they were saluting. They agent were majorly confused.

"Ma'am, I'm Petty officer Lewis, would you like me to show to the captain's cabin?"

"No Petty Officer that will not be required."

"Oh my god, Commander Sheppard, my apologies." He said standing to attention.

"Apology accepted Petty officer.2 with that she walked onwards leaving shocked agents. They stepped into the captain's cabin and she dropped her bags and smiled.

"Jenny Sheppard, ever the more beautiful each time I see you!" said Captain Hoffman.

"Wayne, every the more wrinkled each time I see you."

"Charming! Remind me not be nice next time." He said laughing. She hugged the older man with a smile.

"Captain Hoffman, meet Special agent Jethro Gibbs, Timothy McGee, Tony DiNozzo and Ziva David." The introductions were done and soon it was decided that the investigation would begin tomorrow as it was late. So Tony Ziva and McGee were set a room together whilst Gibbs and Jenny remained.

"Jenny, your own room is empty so you're in there. Gibbs I'm afraid you will have to share with a petty officer."

"Wayne, you said mine was empty."

"IT is Jenny."

"There are two beds, he can stay in with me."

"Jenny-"

"Wayne! It's final. Jethro follow me."

Both men exchanged a glance that showed they had been told. Jethro followed Jenny still not feeling like it was the right time to ask questions. Ashe opened the door on a dorm with two beds on either side. There was a cupboard and the room was impersonal but Gibbs could see it held a lot of memories for the red head. She smirked and took a bed, looking out of the porthole with a smile.

Half an hour later they had unpacked, jenny was sat reading and Jethro watched her. She placed her book down and looked at him. "Jethro, please, we can talk later. Now though I'm tired, and I'm not in the mood."

"Jenny-"

"No, tomorrow night, any other moment but now Jethro. This ship holds memories, and for the moment that is all I am saying."

He didn't push. There was something in her voice that told him not to. She was grateful for that. In her heart she knew this was going to be hard, and she could already feel the layers of her secret being unravelled. It was now only a matter of time…

_**I hope it was okay, please leave me a review! **_

_**-fashiongirl97**_


	2. stepping back into the commander's shoes

_**I don't own ncis**_

_**Oh, my gosh! Thanks so very much for your response, I am overwhelmed, and so amazed, so thank you! **_

_**I-AM-RIVER-SONG : here you go and I am so pleased you love it so thank you so very much. Xx**_

_**Shy Chey 97 : I am so pleased you like it, hope this is just as good **_

_**Paris Never Ends : I am glad you like the idea, I hope this is to your taste too!**_

_**JMI : I am glad you love it, I hope the plot line continues to enthral you **_

_**Ncisgirl2389 : I am glad you enjoyed! I am glad you enjoyed Jenny, and sorry about the spelling.**_

_**Left My Heart Paris : I am so pleased you enjoy the story, and I am glad you hope I am on to a winner! I hope so too! :P**_

_**RhizOniell : glad you enjoyed! Hope it continues to please you! **_

_**Tempe4Booth – I hope it continues to interest you!**_

Jethro awakened from a deep slumber. His eyes adjusted to the greyish light. He was surprised he'd slept so well, he usually didn't when they were on a boat. But maybe it had something to do with the fact he'd been sharing a room with that red head he just couldn't seem to get off his mind. Last night she'd fallen asleep first, he'd just watched he, like he always had when they were undercover. She looked so peaceful in sleep; all the secrets, stress, and worry were gone. The lines that he'd seen form over the last few months were gone. She looked like the old Jen.

He glanced at the clock on the wall, it was 05 30. He also looked up to see Jenny awake. She was dressed which made him a little annoyed he didn't get to watch. She was wearing what he guessed should be figure hugging trousers but instead looked slightly lose. The blue of the trousers matched the blue stripe in her white blouse. Her hair was down. It was growing; he hadn't liked it when she had it short. In his mind it was like the last connection with the old Jenny he had known and loved was gone.

"Morning Jethro." She said with a smirk as she noticed him watching her.

"Morning." He said gruffly. He noticed she had a mug of coffee. He got up intent on pinching it when she handed it to him. He didn't know what had changed, but it was like being on this ship had made her the way she used to be. He didn't know how, or why, but it had, after simply a few hours made him realise how much he still loved her. "Thanks." He said.

Once his coffee was finished he grabbed a towel and was about to leave when she looked at him quizzically. "I'm off for a shower." He replied.

"There is a shower through there." She instructed. HE walked through to find a tiny room with simply a basin, mirror, toilet and shower. There was barely any room but he could tell it was a luxury. As he stood in the shower he began to wonder what exactly this ship meant to Jenny. Why she got the respect she did. He wanted to ask, but in some ways he knew it was none of his business what so ever. When he did come out the bathroom 10 minutes later he found her sat on her bed reading through his case file. HE raised an eyebrow at her only to get a smirk back. Before he could even think of asking she had grabbed her bag and left.

_**-the commander's heart-**_

Jenny looked at the picture in front of her. It was of her and Wayne, both in their dress whites. He had his arm around her, and she was leaning into him and laughing at some joke or something. She remembered it was the day she had become commander. She looked happy, young. She missed this ship, she was sat in her old office at the minute. Getting up she sighed, it looked as though her heart was begging to return, but she didn't know exactly what her head was saying. Standing up she left the office. As she walked along the corridors she still knew so well like the back of her hand. She walked and was met by all different rankings of people saluting. "Petty officer, here now." She said noticing a young girl who was flirting. She signalled for the man to walk away which he did. She stood in front of Jenny slumped shoulders.

"Yeah?"

"It is 'yes ma'am' to you, what is your name?"

"Petty officer 3rd class Kelly George ma'am." She responded.

"Well then petty officer, there are rules on this ship. Stand straight, head up, hair in a bun at the base of your neck with any bangs or find clipped back. I want to see that button done up and if I see you looking not dressed properly again I will have you doing 300 sit ups do I make myself clear?" questioned Jenny, her voice turning al commander-ish again as she slipped back into her role she had played over a decade ago.

"Yes ma'am, won't happen again ma'am."

"Good, I should hope not now be on your way." With a solute the young girl walked away. Jenny smirked at herself as she walked on down.

"You still gonna try and say you don't miss it Jen?" she heard a man shout behind her. She turned around to see the captain.

"Would I convince you if I did?"

"After that? Not a chance Jenny." She just laughed, and made her way to the rooms that ~NCIS were using. As she arrived she stood next to Tony who looked at her as a load of Lieutenants went silent as they walked past. Jenny smirked at his shocked expression.

"SitRep Tony."

"Ah, yeah, sorry Madame Director. Well we have found a ring of people who have connections to our dead sailor. It seems as though there is something going on. We have proved three of them to be innocent; the fourth is in there with Gibbs now. He seems to be the only one who isn't clean."

As Tony spoke Jenny heard the door slam and Gibbs came out looking like he would kill someone. "He's not talking." Jethro said. Jenny looked at him, and took his file, reading it through briefly, memorising the basics quickly.

_Name- Chief Petty Officer Wilkinson_

_1 suspension for not following orders,  
2 warnings for incorrect dress,  
1 case of suspected drug use._

Jenny wondered how the heck he had become a chief petty officer with his record. She quickly decided to get back in the chair and use both her past as a commander and as a field agent and crack him. "I'll have a word." She said looking at them both. She opened the door and stepped in, only Jethro did too. They took the places they had years ago, only this time reversed. He sat in the chair, she stood up.

"Agent Gibbs has some questions for you Wilkinson, you will answer then do you understand?" he just looked up at her.

"Where were you on the night of your friend's death?"

HE didn't say anything.

"You do care about catching the killer?"

Nothing.

"Were you two doing drugs?"

Nothing.

"Were you two selling drugs?"

Nothing.

Jenny stepped forward; she looked at him, and sat on the table."Chief Petty officer, do you know who I am? I am formally Commander Jennifer Sheppard, now Director. Which means whatever way you look at it; I am your superior, which in turn means I can decide your future. Now looking at your record it seems as though you have not exactly behaved. Now, I am going to guess you treasure your title as a chief petty officer, am I right? Which means who would hate to be dishonourably discharged or even, god forbid, but all the way back down to a Seaman recruit, I mean they don't even have an insignia do they?...DO THEY?" she shouted. It had happened again she was back in commander mode.

"No ma'am."

"Were you doing drugs?"

"Yes ma'am."

"Where you selling drugs?"

Nothing.

"WHERE YOU SELLING DRUGS PETTY OFFICER?"

"Yes ma'am."

"Thank you, now did you kill you best friend?"

Nothing.

"Fine, I will inform the captain who is a very good friend of mine you are to be placed back down to a seaman recruit pending further enquiry. Which means everyone is spoken to; it means all the little things are dug up from your past. I don't play games." She said the last bit next to his ear and was about to walk out when he looked up at her.

"It wasn't me ma'am. I don't have a clean record, nor am I clean but there is a line even I won't cross and that is it. You were in the Navy ma'am; you know how much you depend on your friends when you are away for years."

"I do."

"Then you will know how much you depend on them, he was my friend, he was the one I depended on. I wouldn't kill him ma'am."

"Thank you Petty officer." She said before leaving. Jethro looked shocked before walking out. He looked at Jenny who was smiling; he couldn't help but smirk back at her. "He's telling the truth."

"And you are smug."

"Am I not allowed to be?"

"Jen, what he said about-"

"It is in the past. I do not wish for it to be common knowledge Agent Gibbs." He simply nodded, and she walked away.

To say he wasn't proud when she had interrogated the petty officer would be a li. HE was proud she still remembered what he had taught her. Yet to say he didn't feel disheartened that she hadn't told him she was a former Navy commander would also e a lie. But something in the back of his mind told him that just confirmed what they were these days; they were nothing more than colleagues, with a hint of friends. Yet that same voice in the back of his head also told him he still loved her. Maybe this whole thing would bring back the old Jenny; maybe it would confer a few things for both of them. Now he just wanted to hear it come from her lips, he wanted her to tell him about her past, not some dirty Petty officer.

_**I am now a beta! *bows* so if you would like me to help or whatever PM me please :D**_

_**Please continue to review – they make my day ! **_

_**-fashiongirl97**_


	3. Am i really happy?

_**Disclaimer- I don't own ncis**_

_**Authors note – I have to say an amazing thank you to every single one of you, I am so amazed by your response, I really am! I never would have expected it so thank you to all of you!  
I hope this does not disappoint…**_

_**Thank you massively to…**_

_**Left my heart in Paris – thank you, I'm glad you like it, and I hope this is ok too. Xx**_

_**Clochette – thank you so very much! That makes me really happy to know I seems that good so thank you. I miss Jenny too! I'm so pleased you like it and I hope this is ok, sorry for the delay!**_

_**I-AM-RIVER-SONG – I am glad you like it, I am so sorry for the delay, hope this doesn't disappoint.**_

_**RhizOneill – thank you, and I hope this is okay! **_

_**Teardrops of ink – I love writing Jenny is control, she is such fun! Hope you enjoy!**_

_**Paris Never Ends – Hope this doesn't disappoint, and thank you. it is beginning to be public not and no more a secret. Hope it is okay **_

_**NCIS she-demon – thank you for both the reviews! I have actually never seen 'down the periscope' but will try and see it. Hope you enjoy!**_

_**AzNeRd – I'm so pleased you enjoy it, and I'll try update more soon! **_

_**Please keep all your reviews coming, they make my day and enjoy ….**_

They didn't see each other the night that followed Jenny's interrogation of the Petty officer. She'd gone back to the office to deal with paperwork before meeting up with Wayne to go over how to get all the officers respect for NCIS. It was decided early the next morning Jenny would have a word. She had been surprised to find that she still gained respect, and even more than the captain a lot of the time. She knew she owed a lot to Wayne, he'd obviously kept her name flowing around the ship. She had thought that when she came on the ship no one would recognise her. Yet she knew, although it was an honour it was also a slight problem. It meant that she could no longer keep her Naval past a secret, and that in turn would mean questions. Things she didn't know or want to answer.

That night Jenny was already asleep when Jethro got back to their cabin. She looked peaceful, quiet, pleased. He didn't want to disturb her and was too tired to simply admire her beauty. So he lay his head on his pillow and attempted to sleep, the words from the interrogation haunted his mind…

"_I am formally Commander Jennifer Sheppard." _

He couldn't stop thinking about her, thinking about how she had done so much, earned so much respect, all the life she had lead yet he never knew existed. He felt a sense of guild because he had never asked. Yet as he thought, he remembered how much she had known about the navy, even from her first day. She'd known the slang, known the names, her way around a boat, the uniform when she went undercover. It was unbelievable in one way yet made perfect sense in another. He was proud of her. He wished she had told him though, wished more than anything, but then again their relationship had never been based on talking. There was a lot she didn't know, hadn't known until he had lost his memory. But as he lay there that night remembering all of the times from Paris when he had thought they would never be separated, he realised something, he loved her, he always had, and always would.

When Jethro woke up the following morning her bed was made and she was gone. He knew early mornings and messed up sleep schedules were part of a naval officer's everyday life, which meant she would be used to it. He got up, washed and ready and went to wake up his team who would no doubt still be asleep.

Standing outside their room he knocked fiercely on the door. The door was opened by McGee who looked rough as anything. "Boss?" he asked, not quite with it yet.

"Get ready McGee." Gibbs said walking in. He walked in to find one bunk neat and empty, yet the other a mess with covers. On the bottom bunk DiNozzo was sleeping. "Up, DiNozzo! Now!"

"5 more minutes boss." Tony mumbled. Gibbs picked up a glass of water from the bedside cabinet and tipped it over his senior field agent, not in the mood for messing around.

"Aah!" said DiNozzo sitting bold upright and wiping water off of his face. He looked shocked and un-impressed with his boss, although he would never say so.

"Welcome to the Navy DiNozzo."

"Thanks boss." He said sarcastically.

"Where is Ziva McGee."

"Here, Gibbs." Ziva said from behind him. He turned around to see her stood there with a towel over her shoulders, her hair tied sharply back, wearing joggers and a vest top. Her face was shiny with sweat and it looked like she had been to the gym, where ever it was on this ship.

"Right, meet me in our usual room in half an hour." He demanded gruffly before walking out the way he came.

_**-the commander's heart-**_

Down in the NAFFI, the final group of officers stood to attention. At the front Jenny stood, the commander façade and attitude had appeared and she'd instantly gained respect from them all. At the side the Captain stood, a smirk on his face. With ever minute that passed a little bit more of the woman he had known came back. The fun loving Jenny, the loyal Naval officer and the respected and loved commander. She had been strict, everyone knew that, but she had also been the officer who you could talk to. She'd been the person that the Lieutenants would come to and talk about their sweethearts and families to on the long tours, the person young Petty Officers would come to when they thought they could take no more. The thing with Jenny had been she was the kind of person no one would be able to see had a marine, but she was perfect because of that. She had an open mind and would judge no one.

"The agents on this ship are not your enemy – they are your superior. I am not going to tolerate people who find it amusing to sprout 'no comment', and nor will the Captain. We do not fire on this ship, but we will not hesitate to demote. "

Gibbs walked in quietly, after hearing a rumour of what went on. He saw them stood to attention, they he saw the woman at the front. He didn't need to look twice, her red hair, small figure and air of confidence confirmed it was the woman who had plagued his thoughts the previous night. She stood there, demanding the authority she deserved. He saw as men twice her size were taking in what she said. It was then he could see how she missed this job. He saw the glint of happiness in her eyes. She looked glowing and he had a feeling in his gut she wouldn't be returning to NCIS when this trip was over.

"You give the same amount of respect to NCIS as you would to the Captain. If you have information that may aid their investigation then you tell them. If any of you god forbid committed the murder you go to them now. I will say what I said so very many times when I was an agent, if you confess then the charges will be less, if you co-operate the charges will be less. Thank you, Semper Fi." With that Jenny stepped down, they all saluted as she switched places with the Captain. As she did Gibbs left. He didn't want to snoop, it was her life, she would tell him if and when she was ready, and for that he gave her nothing but respect – as he always had.

_**-the commander's heart-**_

For Gibbs the day was filled with interviews, gaining information all promoted by Jenny's speech. Te day gave them new leads that made them all in good mood. They were rushed off their feet but things were moving forward which made it all feel more worth it.

Meanwhile, Jenny stood in the Conference room on board the ship having a video conference with the SecNav. It was small compared to MTAC, and a lot less high tech. But there was a certain sense of safety about the room. In fact for Jenny there had become a sense of safety about the whole ship.

Jenny Stood next to Wayne as they looked at the SecNav. The conference revolved around Jenny, but he knew if he disagreed he had the right to but in, but for the mean time Wayne let the two politicians do their thing.

"It seems you have made quite an impression onboard Jenny. People are talking back in DC and they want you back in the Navy."

"They want to get in my bed sir, it doesn't mean I listen."

"That may be true, but you have a lot of respect Jenny. You have worked your ass off, you have climbed to the top twice Jenny. That ship is still the best in the US Navy and you made it that way."

"We both did."

"That may be the case but I want you back on that ship Jenny. I have since the day you left. Jenny, you are one of the best Commanders this ship has had. You two could become the face of the US Navy, and that is not just my view. I want you two back together."

"I am honoured sir, but if I was to return it would not be for a promotion nor a pay check. "

"I didn't think it would be, but what I will say is that I do believe you could make a massive difference. "

"I would like to think about it if that is okay sir."

"That is fine Jenny, I would like to know by the time I come in two days for the ceremony, if you accept I would like it revealed then."

"Thank you sir."

The line went dead then. Jenny looked to see Wayne smiling at her. "You gonna take it?" he asked.

"I don't know. I…Am I too old? I mean I was young when I left, now…I need to think." He gently hugged her as she left.

_**-the commander's heart-**_

When Jenny returned to her room late that night, Jethro was already there. The offer of returning was weighing heavy on her mind. It wasn't like the opportunity had never been there because it had always been there, it was just she had never truly considered it. Now though, being back on this ship that she had made and which had made her who she is, it made something in her heart scream out. She knew she wasn't happy at the moment; she hadn't been in a long time. She remembered how she had been happy she had been. These days all she had was her job, but then even when that was all she had, the people onboard had become her friends. Now she felt detached from the people she worked with.

Jenny dumped her stuff under her bed, and went into the bathroom, only to emerge in a slouchy outfit of a baggy cotton top and leggings. Jethro still thought she looked amazing, without the make-up and power suits she looked more beautiful. He saw her sit down, but she looked stressed as though she had a lot on her mind. HE put down what he had been looking at and looked at her.

"When I was younger, when it was me and my father, I spent my summers on navy bases. I didn't get on with the navy brats and ended up going to the college. I joined the navy after I finished school. I worked my way up. When I came to this ship, it was awful, no respect, nothing. Between me and Captain Wayne Hoffman we built it up to what it was, the best US Navy Vessel. It still is only not by as much. As a reward I suppose I was promoted again. I worked my way up fastest, and became the best female. I suppose some think ii got it easy, but I put my back into it. I only stayed as commander a year before joining NCIS to get my father's killer. "

"You miss it." It wasn't a statement, but a question.

"for years I told myself no. Every time I would speak to someone who knew me back then they'd asked me to return and I'd laugh it off. But being back onboard, I don't know…something in me has clicked."

"Why didn't you tell me Jenny? You kept it a secret for years, even through Paris any everything." His voice sounded hurt, and it made Jenny question herself as to why. She had excuses, but none of them seemed to fit any more.

"I always told myself it was because I didn't want to be treat differently. Yet as to where you were concerned, I don't know. There are a lot of things we didn't tell each other."

"I know."

They both rested in silence for a while, it hurt to think back to times when they had been so close and then to think of now when they didn't even know if they could call each other friends. A lot had changed since Paris. She had left, but neither had overcome their pride and gone to find the other."

"I shouldn't have lest, for that I apologise." She knew she was breaking a rule, but it needed to be said.

"It takes two people to end a relationship Jen. I should have come after you."

In that moment they caught one another's eyes. It was as if that was all they needed to say, to lay all the wrong and mistakes between them to bed. For some people it may seem stupid, but for them it took guts. Jethro stood up and joined her on her bed; they didn't sit close like lovers, but like friends.

"The SecNav offered me a chance to return. Stay as commander, but move up the ranks, just like all those years ago. This time I actually…I-"

"Consider it Jen. You seem happier now, happier than in a long time." She smirked at him. "What?"

"That, it just, I never thought I'd hear you say something like that Jethro."

"what about I love you?" he questioned.

"Only ever hoped Jethro." She said it like she was shocked – which she was. She couldn't believe her ears. But none the less a smile formed on her lips.

"Well I do, I love you Jenny."

She didn't reply, she couldn't trust herself not to screw it up. So she leaned in an d kissed him. It was slow and sweat and so unlike their first kiss back in Marseilles which had been filled with lust and passion. This one was of true love. When they parted they kept their fore heads close.

"I love you too Jethro."

"That night they sat there, curled up together sharing kisses. It was then Jenny realised that whatever she chose to do, her life would change for the better, and this time, she was not going to lose him.

_**Please keep all your reviews coming, they make my day and let me know I am doing it okay!**_

_**Please review!**_

_**-fashiongirl97**_


	4. time to be honest

_**Disclaimer – I don't own NCIS**_

_**Authors note – Yes you really are believing your eyes, I have updated. Sorry for the delay, I have exams therefore revision which has to come first. Anyway, I hope this chapter is okay, that's so very much for all your response – I'm overwhelmed. I love writing this story. I think I am going to make it into a trilogy instead of one massive long story! Anyway, thanks to….**_

_**I-AM-RIVER-SONG : thank you so very much, I am honoured and amazed you like it, and your stories are amazing, so don't put yourself down!**_

_**Left My Heart In Paris : I'm really glad you like it! You will find out in a matter of minutes, so I hope it doesn't disappoint!**_

_**Shy Chey 97 : I'm glad you like it and thank you **_

_**AzNeRd : hope it's ok, and tell me if you cry or not please! I love having people feel emotion towards my stories!**_

_**Clochette : I love writing Jenny being bossy – it's so fun! And I totally agree, they are so sweat! Hope you continue to enjoy!**_

_**Rhiz Oneill : You will find out if she stays or not in this chapter, so I hope it's ok, and tell me if you cry please! **_

_**Ncisgirl2389 : This chapter had Jenny filling in the blanks in it so you should get any confusion or anything out of the way. But any queries PM me. Hope you enjoy!**_

_**I hope you all enjoy this and thank you so very much, you make me continue to write!**_

It's strange to think that that night was the first night since Paris that they had both gone to sleep content with their lives, the first night they'd slept with smiles on their faces, and neither had awoken in a cold sweat because of the memories that haunted and lingered in their minds. They slept, curled together on that tiny bunk. His arms wrapped around her waist, unwilling to lose her. She kept her head on his shoulder, using it as a pillow like she had all those years ago.

When Jethro awoke the next morning, jenny was still sleeping softly. Slowly he ran his hand through her hair, stroking it like he had done on those few occasions when her past and her memories had been too much for her to take. He watched her in sleep, the lines of aging gone, the façade of strength and coldness gone. But as he did so her eyes fluttered open and in a breathy, still half asleep voice she said "You know I can't sleep when you are watching me Jethro?" he simply laughed, remembering how that had always been the first thing off of her lips in the morning.

"Can't help it Jen." He replied, as he looked at her: green eyes still clouded with sleep, her hair ruffled and natural. Her makeup: nonexistent and the façade gone. She wasn't the director as he watched her now; she wasn't the fiery headed Probie or the loyal daughter. She was Jen, the woman who he had fallen for nearing a decade ago and had never given his heart back. This was the woman he wanted to spend the rest of his life with.

"What time is it?" she questioned, knowing she couldn't just lie here all day – as much as she would love to.

"05 40." He replied. She just smiled and snuggled closer into his embrace. They stayed like that for a while. But as uncommon as it was for him, the silence needed to be broken, because there was an elephant in the room. "Jen? What are you going to do?" he questioned. She looked up, knowing he was talking about her job, simply because it was what had been running through her mind.

"I want to take the job Jethro, but I want to be with you. I don't want my career getting put in front again."

He placed his hand on her cheek and looked deep in her eyes. This was the man she had fallen for: the side of him that so few got to truly see. Those moments: when he was simply Jethro, not the gruff special agent nor the hard as nails ex-marine. When he was the man who wore his scares and had had his heart broken, but loved stronger than anything else. "You do what your heart tells you Jenny. Whether you stay at NCIS or rejoin the Navy, I'll be here. That I promise." He kissed her softly, as if sealing the promise.

They got up shortly after that, showered and changed. By the time Jethro was out the shower Jenny was ready. She stood looking at her old uniform. Memories filling her mind. She was content just to watch her. He saw as a smirk formed on her face and her eyes glazed over, memories filling her head.

_Jenny Sheppard stood there on the deck of the SecNav's boat. It was her first outing with the Navy, and she was stood wearing her dress whites. Her hair taken sharply back - as were the rules. She walked down the table she was sat at with Captain Hoffmann, the director of NCIS, and a few other high ranking officers. As she went to sit down Way_ne _wolf whistled at her. She just laughed and brushed off the complement. "Congratulations on the promotion Commander Sheppard. You have obviously earnt you stripes in the Navy. If you ever feel like a change, NCIS would be gad of your expertise." Said Director Tom Morrow. _

"_Thank you sir." _

_Jenny sat down, a smile on her face. Wayne leaned in to talk to her. "Looking good Jen. How about I spill the red on you and you can go back to your old dress, then you don't have to be here and I can flirt without people thinking we're together." He said winking._

"_I would, only then I wouldn't get to flirt. Sorry." She said with a wicked grin. That evening neither her nor Wayne had had any love interest by the time it can to the last dance. They ended up dancing together, slightly intoxicated they'd done the waltz, pretending to be in love – when they weren't giggling that was._

She felt a presence and turned around to see Jethro. She smiled at him, and shook herself out of the memory. That had been happening a lot lately, she'd been thinking about the old days. Back then a lot of people had thought she and the Captain were sleeping together. They weren't though; it would have been wrong considering they acted like brother and sister or best friends.

"You miss it." He said. IT wasn't a question, more like a statement. He could tell by the way she acted how she'd gazed out the portholes and slid back into commander role so quickly.

"Yeah, more than I ever thought I did." As she looked in his eyes in that moment she knew what her heart was telling her. She had made her decision; this was what she wanted to do.

_**-the commander's heart-**_

She sat in her old office, the light shining in through the small window as she gazed outward. That view, the sea meeting the sky had been one she had gazed at so many times over the years. From the days when the sea was calm, the orange sun sets, from the cold rough winders to the Mediterranean rains. IT had been one which had bared her sorrows and shared her laughs. As she stared out now it distracted her from whatever it was the SecNav was saying on the other end of the phone. She'd told him her decision and he'd accepted it. Now though he was rambling on about some dinner up the hill she was expected at. As he read out the guest list to ignoring ears she wondered how her life was about to change. She had the man of her dreams back. Would she marry? She wondered, it was something she had dismissed the idea of years ago, but now maybe it was a possibility. Jenny knew children were out of the picture, she was too old in her mind now, and she knew neither of their jobs would permit it. Yet they had their 'NCIS' kids, and maybe one day soon they'd have their own kids, and Jenny and Jethro would have grandchildren. With a smiled Jenny attuned her ears to the SecNav.

"…now I'm flying out later on today so I should be there early evening, Then it is just a case of the ceremony tomorrow. You and Special Agent Gibbs did bring your dressage did you not?"

"We did yes sir."

"good. Now I shall see you later on Jennifer, as of now I am being told to pack by my wife."

"Give her my best wishes sir and have a good flight."

After that the call ended. Jenny got up and walked back over to view. It was a clear day outside, the sun was high in the sky and it made her smile to see it reflecting on the sea. The only sound was the one of the bustling officers outside. The corridors were the heart of the everyday activity: Officers getting told to sort out their uniform, others passing on scuttlebutt, while one or two spoke silently about what needed doing. Today was busier that most as the ship prepared for the arrival of the SecNav.

Without a word of warning her door flung open and in walked her agents. She turned around and raised an eyebrow at Jethro. "We've been kicked out. We need a base."

"So you thought you'd us my office?"

"Well unless you can magic us somewhere else, but with the arrival of the SecNav I am guessing not."

She let them have her office for the time they needed. After two hours they had cracked the case, he'd been arrested and detained. The drugs ring had been brought down by Jenny and Wayne and the team were sorting through their paperwork. The former Commander looked up from her paperwork and stared at the team. Jethro met her gaze and he knew what her decision was, and he was proud, but now it was time to tell the team. He silently nodded as she stood up and walked over.

The three agents looked up from their work and looked at their red headed director. "I'm pretty sure by now you've all heard scuttlebutt and what not about me. And obviously after my interrogation the other day which Tony I know you listened in on." He looked scared and rightly received a head slap from his boss.

"Won't happen again, Madame Director." He said, only to get another head slap from her for addressing her as 'Madame'. Jethro just smirked.

"Anyway, I think it's about time I'm honest with you all." She said, and they all stopped and looked at her, she had to contain a laugh, but not the smirk. "When I was young, I used to spend my summers on a naval base. But when I was 14 I got tired of playing with all the other 'Navy Brats' so I managed to get into a Navy college. I trained with all of the seaman's recruits, and passed way above their level. By the time I finished school I'd managed to become a Petty officer 3rd class which was a first in the history. I ended up joining the Navy and in between tours I got them to send me to college.

"I managed to climb up to the rank of Lieutenant, and at that point, Captain Hoffman and I got placed on Destinies peek."

"That's this ship? And he's still the captain right?" questioned Tony.

"Yeah, only back then it was the worst ship in the Navy, I mean it was where all of those people that had friends in high places but were useless officers got sent. But between us we made it what it is today. I was awarded with the Rank of commander and stayed on for another two years before leaving."

They were all shocked. It wasn't just the fact that she had this whole past that no one knew about, but it was the fact she had been so open with them. Jenny was like Jethro in that respect, she would keep her past and her feelings locked away. Ziva looked at her best friend. "Jen, I get the feeling there is something else."

Jenny just laughed, after over 5 years Ziva could still read Jenny. But in the red heads heart there was a wave of guilt. They'd been such good friends back in Cairo and Israel, they'd lived lives and seen the most terrible things, but nothing had separated them. Yet when Jenny had become director that was all it had taken, she'd been the one to put a wedge between them.

_**-the commander's heart-**_

Jenny stood in front of the small mirror in her and Jethro's room doing her make-up. She had guessed that the SecNav would want a black tie meal on his arrival – he always did. So, she had gone by Jethro's rules and been prepared, she'd brought a deep blue dress with her and matching heels. The dress had a heart neckline and long sleeves. It was in typical Navy blue and was fitted to the waist before becoming slightly more lost. It fell just above her knees with her matching heals. She tied hair up seeming a she had not sraighteners or curlers. But as she got ready she spared a glance for Jethro who was sat reading some book in Russian – the one language he knew that she didn't. "Am I doing the right thing Jethro?" she asked, looking at the man who had captured her heart.

"Jenny, you've listened to your heart." He said it as if it were the only thing she needed to hear, but for Jenny things were never that simple.

"My career drove a wedge between us last time; I don't want it to do it again."

"Jen, you are returning to the job you love. I know we will go months without seeing each other, but we'll cope and it'll make our time together more special."

"Leroy Jethro Gibbs, you are an old romantic!" she said smirking. HE just laughed and mock glared at her.

"Don't tell anyone, I have a reputation." He whispered in her ear as he hugged her from behind, making her squeal with laughter. The smile on her face, the glint of happiness in her yet that was stronger than he had ever seen it before made him know they'd cope. It was her smile. Just a simple smile, but it was _her _smile: her bright, happy, cheeky, fun loving smile. A smile he hadn't seen in way too long, one she hadn't worn in way too long that confirmed her decision was the right one.

When the time came for her to go to the dinner, she left the room swaying her hips to wind up Jethro. For him it was like having the old Jenny back, and that was something he would never tire of having. She walked down the 'oh so familiar' corridors that confused most. She saw the SecNav standing, looking slightly confused – something not many people saw him as. She just laughed and walked over.

"Jennifer! I thought you would already be at the table." He said,, covering his confusion.

"I had to have a 'talk' with agent Gibbs." He just laughed and she smiled back. "Would you like to walk with me sir?"

"I hope you are not implying I am lost Director?" he joked.

"Not in a million years sir." She replied in the same tone. It was strange, the way that Jenny could get people to bring down their barriers with just her smile, just her presence. They walked into the room where everyone was sat down and joined them. The meal was a typical one. Everyone was professional, everyone happy. The SecNav stood up to make an announcement and everyone become silent.

"IT's not often that I meet someone who can become the best at everything they do. But I have known one of them people for a long time. Most of you know Jenny Sheppard the Director of NCIS, but she was the best Commander the US Navy has ever had. But there comes time for change in every body's life. So today I want to say that we are all honoured to have Jenny Sheppard returning to the Job she loves in the US Navy." Everybody clapped, and Jenny blushed – how she hated being made to sound like a hero.

"Thank you." She mouthed to him. But the SecNav was not done yet.

"But, she was a commander nearing two decades ago now-"

"-Make me feel old then." She interrupted.

"So, I and the captain did not feel it right for her to carry on where she left off, even if it was at a high level. So, after a lot of discussion I would like to give you this." He said handing Jenny a suite bag. Confused she opened it up, in side was a captain's uniform.

"You're sure?" she asked – shocked.

"100% Jen, you deserve it." Wayne said.

"Thank you." She said. But no one else saw what was inside the bag, nor knew about the promotion. They wouldn't until tomorrow either, no one would.

As Jenny returned to her room that night she found Jethro lying asleep on his bed. She hung up her new uniform and changed into more comfortable cloths. She noticed he'd left space for her on the tiny bed, and with a smirk she joined him. Instinctively he wrapped his arm around her.

"How was he meal?" He asked, sleep filling his voice.

"Fine, go to sleep."

"I love you Jenny."

"I love you too Jethro."

With that, entwined in one another's arms they fell into a peaceful sleep. Their lives would be mad to begin with, but soon they knew they'd get used to it, and Jethro had been right earlier that day: their time spent together would be more precious.

_**Please don't hate me! JIBBS will stay together!**_

_**I hope you enjoyed!**_

_**Please continue to review, you guys are amazing!**_


	5. praise well deserved

_**Disclaimer – I don't own NCIS**_

_**A/N – I am so sorry for the delay – life has gotten in the way! **_

_**Thanks for all your reviews –**_

_**Left my heart in Paris : hope this doesn't disappoint, and love the idea of sailing around the world **_

_**AzNeRd : thank you, I might bring Hollis in in the next story (it's gonna be a triliogy). Hope you continue to enjoy and thanks :D **_

_**Ncisgirl2389 : Everyone known now :P glad you're enjoying xx**_

_**Teardrops of ink : she will continue, but NCIS will experience a lot more twistas and terns in the next story (I'm doing a few more chaps of this one first though). **_

_**RhizOniell : Sorryy…..but I hope this is ok! Enjoy and thanks xx**_

_**I-AM-RIVER-SONG : Sorryyy me update are slow :'( hope this is ok **_

_**Shy Chey 97 : I'm glad they're together :D hope this is ok, and I'm glad no one hates me … yet xx**_

The following morning Jenny and Jethro awoke to a world of madness on board the ship. It was typical really, whenever a ceremony was to take place on the ship everything was to be cleaned and tidied. Jenny got up realising she had better help if she were going to be Captain of this ship, side by side with Wayne. As she tried to get up Jethro pulled her in tight not wanting to let her go. She just smiled, loving the feeling of his arms wrapped around her waist. He didn't know about the promotion yet – none of them did, she was going to keep it a secret. "Jethro!" she said attempting to sound stern.

"Hmmm." He answered as he began trailing kisses up her neck.

"I need to get up!"

"Hmmm."

"As in now!" she demanded laughing. He just began tickling her making her giggles fill the room. It was a sound he would never tire of hearing. He loved seeing her like this…a big smile on her face, carefree and laughing. She looked younger without the weight of an agency on her shoulders. She loved seeing him like he was now as well, fun, care free…it was a sort of honour to get to see the other side of the gruff ex-marine that so few could see. In that moment, separated from a world of deadlines and expectations they were both happy. Jenny and Gibbs knew that no matter what would come, they would be standing together - strong.

Finally she escaped his grasp and ran into the bathroom. She emerged 20 minutes later ready for the day ahead. She wore skinny leg navy blue suit pants, and a loose white shirt that was tucked in with bright red shoes. Her hair long and lose as it would have to be tied up later. As she came out to do her makeup Jethro threw a pillow at her. She glared at him, although the smile as broad as day made it lose all emphasis. "What was that for?"

"You took ages!"

"Jethro, I need my pamper time. And anyway I was only 20 minutes."

"Only!" she threw the pillow back at him and told him to go and get ready. By the time he had come out she was gone and being the Director of NCIS, and he was about to become the federal agent.

_**-the Commander's heart-**_

Soon to be Captain Jenny Shepard stood with Wayne on the front Deck of the ship. The whole morning had been spent instructing Petty Officers how to arrange things, and then telling them how to lay a table in the proper manner. Both Jenny and Wayne had become fed up and given the jobs to the Lieutenants. The SecNav was in the teleconference room on a meeting whilst they stood on the tiny balcony at the front of the ship. It was where weapons had been placed years ago. Now though it was escapism. They both stood there; hand on the railings watching the sea, watching as the white horses were formed and galloped away, and the sun played gently on the metallic surface. Jenny's red hair blew gently in the wind. "I never in a million years would have thought you would have just left everything, and joined NCIS only to become the Director." He said.

"Neither would I, I don't regret it all, parts I do; letting my revenge take over. Not the experience though, not the love nor the laughs."

"Gibbs."

"Yeah, a life time ago in Paris."

"And now." She looked back at him raising an eyebrow. He just smirked back at her. It was like seeing the old Jenny, the one who he had loved to see swanning around the ship and ordering people around with that glint of amusement in her ye. He realised then that being director had not been what she wanted, it was obvious when you compared the woman who would stand in the blacked out room controlling black ops to the one stood next to him. "Don't tell anyone – not yet."

"Cause not. I'm glad you're happy." He said hugging her briefly. They remained silent for a while after that, until Jenny's curiosity took over.

"Did you ever get married Wayne."

"No, I mean I'm too much of a chick magnet to settle down Jen – you should know that!" she just laughed at him. He made her smile, he always did.

"Seriously though?"

"No, it's the one thing I regret I suppose. Remember when you first came, you asked all this stuff about me, claimed you liked to know the people you worked with."

"Yeah…"

"You asked if I had kids, I said no. I always wanted them, always loved children."

"I guess we're both sticklers for letting out careers get in the way."

"That we are Jen."

"Ahh, just the two people I was hoping to find." Said SecNav as he walked out.

"Sir." They both answered standing straight again. He just smirked at how they could go from a calm and meaning full conversation to standing to attention in a flash.

"Jenny, I would like to announce your promotion at ceremony."

"Fine by me sir, should I wear my captains uniform?"

"Of course. Now this ceremony is to celebrate armed forces day, and this ship being one of the Navy's best for over a decade. I trust Agent Gibbs had his dress uniform."

"He does Sir. I have informed Agents DiNozzo, David and McGee that they will have to remain below deck."

"Thank you, they will be able to attend the meal though. I have arranged that they be sat with you, Agent Gibbs, the Captain and myself. I seem to have a feeling they are quite close."

"Sir, they are like a family. Miss Scuito often refers to myself and Agent Gibbs and mummy and daddy. In recent years we have all dealt with a lot, it helps to have people there."

"It does. Go, both of you, go and get ready. The ceremony is to start in an hour and a half."

"Thank you." The two left. And the SecNav stood where they had been only minutes ago and sighed. He saw himself in them both; he'd lived his life for his work and had no one left. Looking at them both he saw how they put their all into their jobs, but didn't let it dictate their lives anymore. He knew that at one point that both had, but now they didn't. As he had looked at jenny he saw a spark of something new in her eyes: love. And he had his suspicions as to whom that love was for.

_**-the commander's heart-**_

Jenny walked into the room where the other three agents had been seeing to see Jethro and team all sat down talking. They all quietened and smiled when they saw her. "SecNav says the ceremony will begin in an hour and a half Jethro. Also Tony, McGee and Ziva you're not permitted to attend due to you not being in the military. But, he had arranged for you to attend the meal that is to follow after. Do you have a suite or smart attire?" They all said they did and Jenny smiled. "Good." She sat down with them and they all continued to talk for a while. It was about nothing of much importance, but it was good for them all just to have a laugh every once in a while. After 50 minutes of talking Jenny and Jethro left to go and get ready. She gave him a kiss on the cheek once they were in a deserted corridor before going to her old office to change as she had moved her new uniform there earlier so Jethro would not notice the difference.

She dressed in the new whites. Tied her red curls up into a sharp bun at the base of her neck. She clipped her fringe back, gently applied her make up like she had been taught all those years ago. You weren't technically allowed it but there was a way to get around that rule, like there was for a lot of rules. As completed her look and opened a cupboard to look in the full length mirror.

He skirt fell just below her knee, she wore 1 ½ "heels which were black, and her top fitted perfect. She smirked at how different she looked now compared to as director. She smiled though, she was happy. This was where she belonged and this was who she was. SecNav had decided Leon Vance was to replace her as director – which neither she nor Gibbs were happy about.

Banishing all thoughts of the agency from her mind she turned around as a knock on the door. She turned around to see the SecNav stood there smiling at her. He was pleased to see her back in the Navy. She had been and incredible agent and a brilliant director but she had always been best in the Navy. He looked at her and saw how she looked younger. The SecNav saw a glimpse of that young Petty Officer that had been brought to his attention all those years ago, before she had been put on the route to fast track and stardom.

"The Ceremony is about to begin. You ready?"

She smiled back at the man who had become like an uncle over the years. "Yeah, time to face the music." They both walked down the corridor. The few volunteering Officers who were manning the ship saluted. One or two who remembered Jenny smiled, and subtly nodded. They walked together to the main area where there were lines of officers. Joining Wayne they walked to the front and stood to attention. She saw Jethro further down the row and sent him a glance. She stood diluting with Wayne next to her. She felt so relaxed, happy, at home in a way.

"This ceremony is being held for Armed forces day. But I've come here for a reason. This ship has been the best ship in the US Navy for over a decade." the SecNav said from the podium. "It wasn't always like this though; many years ago Destinies peak was the worst and most run down ship in the Navy. Yet then came along two people, who are with us today; Wayne Hoffmann and Jennifer Sheppard Transformed this ship into what it is today. They gained their respect and got this ship up to the top. Without them, you would all be spread across the world serving your country…" Jenny felt proud of not herself but Wayne. It was him who had kept the ship on the map when she had gone, and it was an achievement. She was brought from her thoughts by the Vicar.

"We are gathered here today to remember those who serve their country and people day in day out and sacrificed their lives so we could lead the lives we do today. Let us bow our heads in prayer. Our father who aren't in heaven, hallow be thy name. Thy Kingdom come as thy will be done on earth as it is in heaven. Give us this day our daily bread and forgive us from trespasses, as we forgive those who trespass against us. And forgive us from evil, for thyne is the kingdom, the power and the glory, forever and ever, Amen. Lord, protect those who protect our country, take care of those who pass from our world into heaven. Amen"

"Thank you. There is another reason today is special. One woman made this ship what is is then went on to transform NCIS and rise it up the ladder. Now she is going to return to where her heart is. Only this time, she won't be Commander, she'll be Captain. I also want to award Captain Jennifer Sheppard with an award for honouree service. She had worked for the Navy for nearing two decades, and I hope it will be for many more too."

Jenny smiled and walked up onto the stage to receive her medal. The celebrations continued and after an hour they all managed to sit down for the meal As Jenny went over to the table she was suddenly smiling. She was about to sit down when Jethro, McGee, Tony and Ziva all just clapped. She blushed before hugging her friends. When Jethro was the only one left she was surprised he hugged her. "I'm proud of you Jenny." He whispered in her ear. They didn't kiss or anything, just hugged like friends.

They all sat down, and they spent the meal smiling and laughing. They talked about how tomorrow they would fly home, and what would happen when Jenny left. The next week Jenny would be at home, then her new life would begin with Jethro by her side.

_**There will be another 2-3 chaps of this story before moving on to 'the captains heart'. This will be a trilogy. :D**_

_**Hope it was okay.**_

_**Please reviews, they make me smile soooooo much! **_

_**-fashiongirl97 xxxx**_


	6. one door closes and another opens

_**Disclaimer – I don't own NCIS**_

_**Authors Note – this is the end of the commander's heart, thank you for all your reviews…**_

_**NCISgirl2389 : thank you! I'm glad you enjoyed it, look out for the next instalment of the trilogy! **_

_**Left my heart in Paris : I'm glad you're enjoying, hope this doesn't disappoint!**_

_**GIBBSandRYANxxx : I'm glad you are enjoying, look out for # 2 in the trilogy!**_

_**Shy Chey 97 : Thank you soo much! I'm glad you don't hate me but there will be twists and turns. Hope continue to stick with me! **_

_**Teardrops of ink : Glad you're enjoying, and I hope this doesn't disappoint**_

_**Rhiz Oneill : Glad you're enjoying…**_

_**Thank you all so so much, and to all of you who have favourite and alerted! Enjoy….**_

This was it, they were back in DC and her new life was going to begin in just a few days. They had arrived home at 11 00 hours the day after the ceremony. They'd been leant the SecNav's plane for the one and a half hour flight. Now though, they were all back in NCIS. The man they had arrested was currently down in interrogation with Jethro whilst the others did their case reports. Jenny however was upstairs empting her desk. She'd decided they she would hand over to Leon today. The agency had already been told about the change and Leon Vance had a smug look on his face. She had just put the final photo frame in her bag when he entered – chewing one of those insufferable cocktail sticks. "Jenny." He stated, eyeing her up.

"Leon." She replied with a hint of disgust – she had never liked the man.

"You took the job then - guess there is only so long you can deal with those up the hill, being a woman and all. Thought you would have hung on a bit longer though, not taken the first lousy job offer that came."

"Excuse me?"

"You know, taking the job as captain, bit of a demotion isn't it."

"Leon, firstly by no way is it a demotion. I am taking a job I love. I have brought things to NCIS and made things happen that you will never be able to. I was the one who dug this agency out of the ground, who made us go up the federal food chain. I climbed the ladder faster and with fewer mistakes than you ever did Leon. I transformed this agency, and now I am going to the Navy, I'll support our country. If you think that is a demotion then think again, and just so you know I will always have more respect from the SecNav, from this agency and every other person 'up the hill' than you ever will." With that she picked up her bag and was about to leave before turning around. "Leon, just to say: you have an amazing agency, with amazing people, don't screw it up or else you'll have me on your ass before you can blink." She gave him a sickeningly sweet smile before walking away. As she left she passed Cynthia and decided she should stop and talk to the woman who had helped her out so much over the past three years.

"You'll be missed ma'am."

"Call me Jenny Cynthia. And thank you. I'll miss you all."

"I respect you for what you are doing, we all do. Taking a job you love, it's…it's the right thing to do."

"Thank you Cynthia, and I mean that. Thank you for the last three years, all your attempts to stop Jethro and for putting up with me when I deserved a lot less."

"You are welcome. I would do it all over again."

"Good luck Cynthia, with your life and dealing with him." She said signalling to the director's office. "If you ever need anything then just remember you are always part of what I suppose is a family now."

"Thank you, and good luck to you too Jenny. You deserve it."

With that Jenny went down stairs. She walked toward the 'oh so familiar' area of the bull pen where her 'favourite' team were. Tony was flirting on the phone to someone most likely half his age and she decided to do what she had wanted to do ever since she started at NCIS and Abby first called her mummy. She walked behind the younger man, head slapped him Gibbs style before taking the phone. "Hello, I'm Tony's…mother, I know I sound too young but it's true. Anthony Jr. has work to do; I do hope you will let him get on with it. Also, how old did he tell you he was?...yes I thought as much he is actually nearing 40…yes I will make sure to pass that on, thank you." She said in a posh and sweet voice before putting down the pone. Ziva was in hysterics and so was McGee. Tony looked shocked and as if he couldn't believe his eyes. "She tells to tell you if you dare ring her again she will have you arrested for harassment." She said going backing to her normal tone before smirking.

"I am not nearly 40!"

"NO, but she is half your age."

"You harassing my agents again Jen?" questioned Jethro as he came walking into the bull pen before standing next to her.

"Thought that one last time wouldn't hurt"

"Hmm…" he said before slapping Tony's head.

"OW! Boss what was that for?"

"Get to work DiNozzo!"

_**-the commander's heart-**_

Hours later at Jenny's house she sat in her study. She sat looking at the photo of her and her father, tears burning in her eyes. He would be proud of her she thought, hoped. Maybe he'd be disappointed she had left in the first place, but she knew he would approve of Jethro. It was hard for her to think of the alternate universes. Maybe if she had stayed she would still have met him on a case, then again she doubted it. Although she did regret letting her revenge take over, she didn't regret everything. She didn't regret meeting Jethro, falling in love, having a sort of miss-fitted family that she knew soon would be her life line, and the thing that kept her and Jethro sane. HE was in the kitchen sorting out something to eat whilst she sat in the study – reminiscing.

There was a lot in her life that she wished that she had done, she wished that she had had a family, gotten the chance to be a mother and get married. Some may think that she still had a chance, still had time ahead. But she knew it would never happen, in her heart. She doubted she'd get married to Jethro. But if she was honest it didn't upset her. There may be things she hadn't done, but now she was taking back control of her life and that was something she was happy about.

_**-the commander's heart-**_

The week had been spent as a family. Jenny had always seemed to be the ever missing figure In the get together of the team. Yet now she was no longer their boss, yet nor was she the captain yet. So in the week she had on leave she re formed the friendships that she had broken. She became best friends once more with Ziva, managed to mend the rift between herself and Tony caused by the undercover op. Most of although she became the mother to the team Abby had wanted her to be. Yet, as the Sunday came around it all seemed to hit everyone. Jenny was being deployed for six months. She stood at the airport awaiting the plane to take her on the ship.

She stood there in her uniform, Jethro stood with his arm around her. She rested her head on his shoulder before hugging everyone else. As she hugged each person she whispered something.

First was Abby "Keep him smiling Abs."

"Always." She replied, a tear rolling down her cheek.

To Tony she said "Keep him safe." To McGee she said "You're a great agent Tim." To Ducky "Don't let him go off of the rails again Duck."

"It was Jethro that walked her to the gate, hugged her tightly and kissed her passionately. IT was only six months, but it would be a six months that would test all of their limits…

_**Thanks for reading! **_

_**Please keep an eye out for '**__the Captain's heart__**' which will be published soon.**_

_**Please leave me a review! I'd love to get this to 50 if possible! Thank you again, and I hope you'll read the next story!**_


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